An introduction to proteins

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 Topic Outline
• Protein functions

• Protein structure

Hemoglobin, with hemes (O2 carriers) in red

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What functions do proteins serve?
• General Answer:
– Lipids, carbohydrates, and nucleic acids are
important, but largely inert and structurally
limited on their own.
– Proteins can form an infinite variety of shapes and
higher-order structures, which can respond rapidly to
subtle modifications.
– The dynamics of protein structure and activity
control almost everything that we associate with
cellular function

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Proteins are abundant

– 50% of dry mass of the cell

– >10,000 different proteins in a “typical” cell
– Different cell types defined by their protein profile

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 Protein Functions
• Catalysts
• Structure
• Communicatio
n
• Transport
• Motility
• Defense
• Recognition
• Regulation
• Storage 5
 Protein Structure
• Proteins are unbranched polymers
– Monomer is the Amino Acid.

• There are 20 different amino acids.

• The ability to vary both amino acid sequence and

overall length enable countless potential proteins.

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How many different 2-residue peptides could exist?

aa1-aa2

• 20 possible amino acids at position 1

• 20 possible amino acids at position 2
• Any given a.a. at position 1 has 20 possible partners at position 2
• 20 x 20, 202, or 400 possibilities

General solution for peptide of length N is 20N

For N=100, there are 1.3 x 10130 possibilities (most proteins >100 a.a.).
Individual (free) amino acid Structure

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Individual (free) amino acid Structure

• The non-R (“backbone”) structure is identical for 19 of

20 amino acids (exception is proline)
• Chemical and physical properties of amino acids
determined by the structure of the “R Group” 9
Free amino acids ionized
in most cell conditions

• two charged groups, but net charge is zero

(a zwitterion)

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Meet the Amino Acids

It is worth
memorizing
these: the
biological
equivalent of
times tables.

Good time to
break out
those flash
cards!

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Charged Amino Acids

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Polar Uncharged Amino Acids

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Nonpolar (=hydrophobic)
Amino Acids

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 Special Case Amino
Acids

• Cysteine: can forms S-S (thiol) bridges with other

cysteines
• Glycine: only H atom for R group
• Proline: bonded to the amino acid N to form a ring
(and kink in backbone) 15
Polymer
Formation

Dehydratio
n Synthesis

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 Polymer
Formation

Dehydratio
n Synthesis

Polymer = Polypeptide
Like nucleic acids, polypeptides have polarity. 17
 Polypeptide vs.
• Similar but not equivalent terms
Protein
• Polypeptide: Linear sequence of covalently bonded
amino acids. Could be a fragment of something
larger.
• Protein: One or more complete polypeptides folded
into a specific 3D conformation. Thus, some
proteins have polypeptide subunits.

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 Protein Conformation and
• Function
Function requires specific shape
• Most proteins fold spontaneously into a specific
conformation.
• Globular

• Fibrous

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 Four Levels of Protein
•Structure
Primary
• Secondary
• Tertiary
• Quaternar
y

1º 2º 3º 4º
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 Primary Structure

• Genetically determined linear sequence of amino

acids
• Depicted as text in peptide sequences and
alignments
• always written from N-terminus to C-terminus
N arginine-valine-proline C = Arg-Val-Pro = RVP
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human & fish actin peptides aligned
N-terminus (amino group free)

C-terminus
(carboxylic acid group free)
 Secondary Structure

• Stabilized by hydrogen bonds within the

backbone
• Can be prevented or facilitated by particular
sequences of R groups.

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 Tertiary
Structure
Molecular interactions
between R groups
within the same
polypeptide.

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 Disulfide Bonds in Protein
When two Cysteine amino acid residues come
close together, their sulfur atoms may form a
covalent Disulfide (S-S) Bond.

• Extremely
stable
• Lock proteins
into shape
• Can form
within or
between 25
polypeptides
 Quaternary Structure
• Only found in multisubunit
proteins
• Dimers! Trimers! Tetramers!
Filaments!

Transthyretin 26
 Protein Folding

• Usually occurs simultaneously with synthesis

• What determines the final form?
– Final form determined by energetic and
entropic considerations
• What does this mean?
– Structures that minimize internal energy are
favored

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 Protein Folding
• What conditions affect the final structure?
– Temperature, Ionic strength, pH
• The shape of proteins is affected by
changing conditions
• All necessary information often be
contained in the 1° sequence

Q: How can we know this?

A: You do an experiment
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Spontaneous Folding in Isolation

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Spontaneous Folding in Isolation

Pure preparations of small proteins often renature easily.

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Spontaneous Refolding Not
Always Possible

X 31
Spontaneous Refolding Not
Always Possible

X 32
 Protein Folding
• “Correct” folding not always spontaneous interaction
• May need help from “chaperone” proteins
• Ex: Bacterial Chaperonins

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 Protein Folding and Disease
• Misfolded proteins cause many common disorders.
– Result from mutations or disruption of normal
folding processes
– Often worsen with age
• examples:
– Cystic Fibrosis – Alzheimer’s Disease
– Parkinson’s Disease – Mad Cow Disease
– Progr. Supranuclear – Emphysema
palsy (PSP)

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 Protein Structure and
• Function
Sickle Cell Disease (Anemia)
– One amino acid change (of 146 a.a.) in hemoglobin
polypeptide

• Why is this change

significant?
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Protein Structure and
Function
• Polar and charged side chain changed to
a nonpolar side chain
– Changes intramolecular interactions
– Changes overall protein structure
– Interferes with the way the proteins pack in
the cell

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37
Sickle-shaped RBCs don’t flow through capillaries smoothly
Effect made worse when hemoglobin less bound to oxygen (e.g high altitude)
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Protein modifications that
alter structure and function

- ligand binding
- covalent R-group modification
- addition of cofactors
- proteolytic cleavage

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Example:
Estrogen receptor is activated by binding of estrogen hormone ligand.
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• most common type: phosphorylation

• protein kinase: enzyme that adds phosphate to R groups of

serine, threonine, or tyrosine

• protein phosphatase: removes phosphates 41

threonine phosphorylation

threonine kinase

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 A cofactor is
generally a
constant feature of
a protein’s
structure.

(ligands come on
and off)

Examples:
• Iron and heme allow hemoglobin to carry oxygen in the blood.
• Kinases have a different shape when bound to ATP vs. bound to
ADP. Their interaction with a substrate changes after phosphate
transfer.
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44
Proteolysis
can also CELL A
create a
signal in a
cell.

Notch
proteolysis helps
embryonic cells
communicate

CELL B

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